Publications: Review Articles
674. Computational methodologies for real-space structural refinement of large macromolecular complexes. Boon Chong Goh, Jodi A. Hadden, Rafael C. Bernardi, Abhishek Singharoy, Ryan McGreevy, Till Rudack, C. Keith Cassidy, and Klaus Schulten. Annual Review of Biophysics, 45:253-278, 2016.
656. Molecular dynamics simulations of large macromolecular complexes. Juan R. Perilla, Boon Chong Goh, C. Keith Cassidy, Bo Liu, Rafael C. Bernardi, Till Rudack, Hang Yu, Zhe Wu, and Klaus Schulten. Current Opinion in Structural Biology, 31:64-74, 2015.
649. Multiple-replica strategies for free-energy calculations in NAMD: Multiple-walker adaptive biasing force and walker selection rules. Jeffrey Comer, James Phillips, Klaus Schulten, and Christophe Chipot. Journal of Chemical Theory and Computation, 10:5276-5285, 2014.
648. Die Geheimnisse des Lebens berechnen. Till Rudack, Juan Perilla, and Klaus Schulten. Spektrum der Wissenschaft, 11:86-95, November 2014.
621. Quantum biology of retinal. Shigehiko Hayashi and Klaus Schulten. In Masoud Mohseni, Yasser Omar, Greg Engel, and Martin B. Plenio, editors, Quantum Effects in Biology, pp. 237-263. Cambridge University Press, 2014.
620. A chemical compass for bird navigation. Ilia A. Solov'yov, P. J. Hore, Thorsten Ritz, and Klaus Schulten. In Masoud Mohseni, Yasser Omar, Greg Engel, and Martin B. Plenio, editors, Quantum Effects in Biology, chapter 10, pp. 218-236. Cambridge University Press, 2014.
619. Structure, function, and quantum dynamics of pigment-protein complexes. Ioan Kosztin and Klaus Schulten. In Masoud Mohseni, Yasser Omar, Greg Engel, and Martin B. Plenio, editors, Quantum Effects in Biology, pp. 123-143. Cambridge University Press, 2014.
609. The mechanism of ubihydroquinone oxidation at the Qo-site of the cytochrome bc1 complex. Antony R. Crofts, Sangjin Hong, Charles Wilson, Rodney Burton, Doreen Victoria, Chris Harrison, and Klaus Schulten. Biochimica et Biophysica Acta, 1827:1362-1377, 2013.
579. Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method. Kwok-Yan Chan, Leonardo G. Trabuco, Eduard Schreiner, and Klaus Schulten. Biopolymers, 97:678-686, 2012.
576. How quantum coherence assists photosynthetic light harvesting. Johan Strumpfer, Melih Sener, and Klaus Schulten. Journal of Physical Chemistry Letters, 3:536-542, 2012.
552. 3rd generation DNA sequencing with a nanopore. Gregory Timp, Utkur Mirsaidov, Winston Timp, Jiwook Shim, Deqiang Wang, Valentin Dimitrov, Jan Scrimgeour, Chunchen Lin, Jeffrey Comer, Anthony Ho, Xueqing Zou, Aleksei Aksimentiev, and Klaus Schulten. In Samir M. Iqbal and Rashid Bashir, editors, Nanopores: Sensing and Fundamental Biological Interactions, chapter 12, pp. 287-312. Springer, Berlin, 2011.
549. Förster energy transfer theory as reflected in the structures of photosynthetic light harvesting systems. Melih Sener, Johan Strümpfer, Jen Hsin, Danielle Chandler, Simon Scheuring, C. Neil Hunter, and Klaus Schulten. ChemPhysChem, 12:518-531, 2011.
545. Molecular origin of the hierarchical elasticity of titin: simulation, experiment and theory. Jen Hsin, Johan Strümpfer, Eric H. Lee, and Klaus Schulten. Annual Review of Biophysics, 40:187-203, 2011.
544. The light-harvesting apparatus in purple photosynthetic bacteria, introduction to a quantum biological device. Johan Strümpfer, Jen Hsin, Melih Sener, Danielle Chandler, and Klaus Schulten. In Benoit Roux, editor, Molecular Machines, chapter 2, pp. 19-48. World Scientific Press, 2011.
543. Viewing the mechanisms of translation through the computational microscope. James Gumbart, Eduard Schreiner, Leonardo G. Trabuco, Kwok-Yan Chan, and Klaus Schulten. In Joachim Frank, editor, Molecular Machines in Biology, chapter 8, pp. 142-157. Cambridge University Press, 2011.
540. Fast molecular electrostatics algorithms on GPUs. David J. Hardy, John E. Stone, Kirby L. Vandivort, David Gohara, Christopher Rodrigues, and Klaus Schulten. In Wen-mei Hwu, editor, GPU Computing Gems, chapter 4, pp. 43-58. Morgan Kaufmann Publishers, 2011.
539. GPU-accelerated computation and interactive display of molecular orbitals. John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort, and Klaus Schulten. In Wen-mei Hwu, editor, GPU Computing Gems, chapter 1, pp. 5-18. Morgan Kaufmann Publishers, 2011.
538. GPU algorithms for molecular modeling. John E. Stone, David J. Hardy, Barry Isralewitz, and Klaus Schulten. In Jack Dongarra, David A. Bader, and Jakub Kurzak, editors, Scientific Computing with Multicore and Accelerators, chapter 16, pp. 351-371. Chapman & Hall/CRC Press, 2011.
537. Immersive molecular visualization and interactive modeling with commodity hardware. John E. Stone, Axel Kohlmeyer, Kirby L. Vandivort, and Klaus Schulten. Lecture Notes in Computer Science, 6454:382-393, 2010.
533. GPU-accelerated molecular modeling coming of age. John E. Stone, David J. Hardy, Ivan S. Ufimtsev, and Klaus Schulten. Journal of Molecular Graphics and Modelling, 29:116-125, 2010.
527. Challenges in protein folding simulations. Peter L. Freddolino, Christopher B. Harrison, Yanxin Liu, and Klaus Schulten. Nature Physics, 6:751-758, 2010.
519. Self-assembly of photosynthetic membranes. Jen Hsin, Danielle E. Chandler, James Gumbart, Christopher B. Harrison, Melih Sener, Johan Strumpfer, and Klaus Schulten. ChemPhysChem, 11:1154-1159, 2010.
517. Multi-scale simulations of membrane sculpting by N-BAR domains. Ying Yin, Anton Arkhipov, and Klaus Schulten. In Philip Biggin and Mark Sansom, editors, Molecular Simulations and Biomembranes: From Biophysics to Function, chapter 6, pp. 146-176. Royal Society of Chemistry, 2010.
506. Discovery through the computational microscope. Eric H. Lee, Jen Hsin, Marcos Sotomayor, Gemma Comellas, and Klaus Schulten. Structure, 17:1295-1306, 2009.
495. Molecular dynamics simulations of membrane channels and transporters. Fatemeh Khalili-Araghi, James Gumbart, Po-Chao Wen, Marcos Sotomayor, Emad Tajkhorshid, and Klaus Schulten. Current Opinion in Structural Biology, 19:128-137, 2009.
488. Modeling transport through synthetic nanopores. Aleksei Aksimentiev, Robert K. Brunner, Eduardo Cruz-Chu, Jeffrey Comer, and Klaus Schulten. IEEE Nanotechnology, 3:20-28, 2009.
475. Exploring the possibilities for radical pair effects in cryptochrome. Ilia A. Solov'yov, Danielle Chandler, and Klaus Schulten. Plant Signaling and Behavior, 3:676-677, 2008.
471. From atomic-level structure to supramolecular organization in the photosynthetic unit of purple bacteria. Melih K. Sener and Klaus Schulten. In C. Neil Hunter, Fevzi Daldal, Marion C. Thurnauer, and J. Thomas Beatty, editors, The Purple Phototrophic Bacteria, volume 28 of Advances in Photosynthesis and Respiration, pp. 275-294. Springer, 2008.
464. Understanding structure and function of membrane proteins using free energy calculations. Christophe Chipot and Klaus Schulten. In Eva Pebay-Peyroula, editor, Biophysical analysis of membrane proteins. Investigating structure and function, pp. 187-211. Wiley, Weinheim, 2008.
462. Molecular modeling of the structural properties and formation of high-density lipoprotein particles. Amy Y. Shih, Peter L. Freddolino, Anton Arkhipov, Stephen G. Sligar, and Klaus Schulten. In Scott Feller, editor, Current Topics in Membranes: Computational Modeling of Membrane Bilayers, chapter 11, pp. 313-342. Elsevier, 2008.
461. Application of residue-based and shape-based coarse graining to biomolecular simulations. Peter L. Freddolino, Anton Arkhipov, Amy Y. Shih, Ying Yin, Zhongzhou Chen, and Klaus Schulten. In Gregory A. Voth, editor, Coarse-Graining of Condensed Phase and Biomolecular Systems, chapter 20, pp. 299-315. Chapman and Hall/CRC Press, Taylor and Francis Group, 2008.
459. Biomolecular modeling in the era of petascale computing. Klaus Schulten, James C. Phillips, Laxmikant V. Kalé, and Abhinav Bhatele. In David Bader, editor, Petascale Computing: Algorithms and Applications, pp. 165-181. Chapman and Hall/CRC Press, Taylor and Francis Group, New York, 2008.
457. Computer modeling in biotechnology, a partner in development. Aleksei Aksimentiev, Robert Brunner, Jordi Cohen, Jeffrey Comer, Eduardo Cruz-Chu, David Hardy, Aruna Rajan, Amy Shih, Grigori Sigalov, Ying Yin, and Klaus Schulten. In Protocols in Nanostructure Design, Methods in Molecular Biology, pp. 181-234. Humana Press, 2008.
444. Single-molecule experiments in vitro and in silico. Marcos Sotomayor and Klaus Schulten. Science, 316:1144-1148, 2007.
433. Molecular dynamics methods for bioelectronic systems in photosynthesis. Ioan Kosztin and Klaus Schulten. In Thijs Aartsma and Joerg Matysik, editors, Biophysical Techniques in Photosynthesis II, volume 26 of Advances in Photosynthesis and Respiration, pp. 445-464. Springer, Dordrecht, 2008.
419. Molecular mechanisms of cellular mechanics. Mu Gao, Marcos Sotomayor, Elizabeth Villa, Eric Lee, and Klaus Schulten. Physical Chemistry - Chemical Physics, 8:3692-3706, 2006.
418. PcrA helicase, a molecular motor studied from the electronic to the functional level. Markus Dittrich, Jin Yu, and Klaus Schulten. Topics in Current Chemistry, 268:319-347, 2006.
408. The role of molecular modeling in bionanotechnology. Deyu Lu, Aleksei Aksimentiev, Amy Y. Shih, Eduardo Cruz-Chu, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. Physical Biology, 3:S40-S53, 2006.
399. Biomolecular modeling using parallel supercomputers. Laxmikant V. Kale, Klaus Schulten, Robert D. Skeel, Glenn Martyna, Mark Tuckerman, James C. Phillips, Sameer Kumar, and Gengbin Zheng. In S. Aluru, editor, Handbook of computational molecular biology, pp. 34.1-34.43. Taylor and Francis, 2005.
397. Molecular dynamics simulations of proteins in lipid bilayers. James Gumbart, Yi Wang, Alekseij Aksimentiev, Emad Tajkhorshid, and Klaus Schulten. Current Opinion in Structural Biology, 15:423-431, 2005.
395. Beyond the gene chip. J. B. Heng, A. Aksimentiev, C. Ho, V. Dimitrov, T. Sorsch, J. Miner, W. Mansfield, K. Schulten, and G. Timp. Bell Labs Technical Journal, 10:5-22, 2005.
384. Kinetic theory and simulation of single-channel water transport. Emad Tajkhorshid, Fangqiang Zhu, and Klaus Schulten. In S. Yip, editor, Handbook of Materials Modeling, Vol. I: Methods and Models, pp. 1797-1822. Springer, Netherlands, 2005.
382. Physical principles of efficient excitation transfer in light harvesting. Melih Sener and Klaus Schulten. In David L. Andrews, editor, Energy Harvesting Materials, pp. 1-26. World Scientific, Singapore, 2005.
381. Towards understanding membrane channels. Emad Tajkhorshid, Jordi Cohen, Aleksij Aksimentiev, Marcos Sotomayor, and Klaus Schulten. In Boris Martinac and Andrzej Kubalski, editors, Bacterial ion channels and their eukaryotic homologues, pp. 153-190. ASM Press, Washington, DC, 2005.
368. Computational studies of membrane channels. Benoit Roux and Klaus Schulten. Structure, 12:1343-1351, 2004.
353. Modeling DNA loops using continuum and statistical mechanics. Alexander Balaeff, Christophe R. Koudella, L. Mahadevan, and Klaus Schulten. Philosophical Transactions of the Royal Society of London A. (Mathematical, Physical and Engineering Sciences), 362:1355-1371, 2004.
348. Molecular biomimetics: nanotechnology through biology. Mehmet Sarikaya, Candan Tamerler, Alex K. -Y. Jen, Klaus Schulten, and François Baneyx. Nature Materials, 2:577-585, 2003.
340. Large scale simulation of protein mechanics and function. Emad Tajkhorshid, Aleksij Aksimentiev, Ilya Balabin, Mu Gao, Barry Isralewitz, James C. Phillips, Fangqiang Zhu, and Klaus Schulten. In Frederic M. Richards, David S. Eisenberg, and John Kuriyan, editors, Advances in Protein Chemistry, volume 66, pp. 195-247. Elsevier Academic Press, New York, 2003.
334. Unfolding of titin domains studied by molecular dynamics simulations. Mu Gao, Hui Lu, and Klaus Schulten. Journal of Muscle Research and Cell Motility, 23:513-521, 2002.
322. Quasicontinuum representations of atomic-scale mechanics: From proteins to dislocations. Rob Phillips, Markus Dittrich, and Klaus Schulten. Annual Review of Materials Research, 32:219-233, 2002.
317. Photosynthetic apparatus of purple bacteria. Xiche Hu, Thorsten Ritz, Ana Damjanović, Felix Autenrieth, and Klaus Schulten. Quarterly Reviews of Biophysics, 35:1-62, 2002.
316. The quantum physics of photosynthesis. Thorsten Ritz, Ana Damjanović, and Klaus Schulten. ChemPhysChem, 3:243-248, 2002.
307. Steered molecular dynamics and mechanical functions of proteins. Barry Isralewitz, Mu Gao, and Klaus Schulten. Current Opinion in Structural Biology, 11:224-230, 2001.
306. Physik der Photosynthese. Thorsten Ritz and Klaus Schulten. Physikalische Blaetter, 57:49-53, 2001.
303. Steered molecular dynamics investigations of protein function. Barry Isralewitz, Jerome Baudry, Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten. Journal of Molecular Graphics and Modeling, 19:13-25, 2001. Also in Protein Flexibility and Folding, L. A. Kuhn and M. F. Thorpe, editors, Biological Modeling Series (Elsevier).
299. To students contemplating research in biomolecular modelling. Klaus Schulten. Journal of Molecular Graphics and Modeling, 18:218-220, 2000.
297. Electron transfer: Exploiting thermal motion. Klaus Schulten. Science, 290:61-62, 2000.
292. The fast multipole algorithm. John Board and Klaus Schulten. IEEE Computational Science & Engineering, 2:56-59, 2000.
291. Group report: How does complexity lead to an apparently simple function? K. Moffat, J.-P. Changeux, D. M. Crothers, H. Grubmueller, G. U. Nienhaus, M. U. Palma, F. G. Parak, K. Schulten, and A. Warshel. In H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, editors, Simplicity and Complexity in Proteins and Nucleic Acids, pp. 255-280, Berlin, 1999. Dahlem University Press.
278. Algorithmic challenges in computational molecular biophysics. Tamar Schlick, Robert Skeel, Axel Brünger, Laxmikant Kalé, John A. Board Jr., Jan Hermans, and Klaus Schulten. Journal of Computational Physics, 151:9-48, 1999.
268. From simplicity to complexity and back: Function, architecture and mechanism of light harvesting systems in photosynthetic bacteria. Klaus Schulten. In H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, editors, Simplicity and Complexity in Proteins and Nucleic Acids, pp. 227-253, Berlin, 1999. Dahlem University Press. (pdf available from author upon request).
256. Avoiding algorithmic obfuscation in a message-driven parallel MD code. James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal Krawetz, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten. In P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, S. Reich, and R. D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, volume 4 of Lecture Notes in Computational Science and Engineering, pp. 472-482. Springer-Verlag, 1998.
255. Steered molecular dynamics. Sergei Izrailev, Sergey Stepaniants, Barry Isralewitz, Dorina Kosztin, Hui Lu, Ferenc Molnar, Willy Wriggers, and Klaus Schulten. In P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich, and R. D. Skeel, editors, Computational molecular dynamics: challenges, methods, ideas, volume 4 of Lecture notes in computational science and engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
248. How nature harvests sunlight. Xiche Hu and Klaus Schulten. Physics Today, 50:28-34, 1997.
221. Probing protein motion through temperature echoes. Klaus Schulten, Hui Lu, and Linsen Bai. In Henrik Flyvbjerg, John Hertz, Mogens H. Jensen, Ole G. Mouritsen, and Kim Sneppen, editors, Physics of Biological Systems: From Molecules to Species, Lecture Notes in Physics, pp. 117-152. Springer, 1997.
217. Topology representing maps and brain function. Klaus Schulten and Michael Zeller. In Nova Acta Leopoldina NF, volume 72, pp. 133-157. Jahresversammlungsband, 1996.
214. Curve crossing in a protein: Coupling of the elementary quantum process to motions of the protein. Klaus Schulten. In D. Bicout and M. J. Field, editors, Proceedings of the Ecole de Physique des Houches, pp. 85-118, Paris, 1995. Les Editions de Physique, Springer.
210. Molecular dynamics studies of bacteriorhodopsin's photocycles. Klaus Schulten, William Humphrey, Ilya Logunov, Mordechai Sheves, and Dong Xu. Israel Journal of Chemistry, 35:447-464, 1995.
196. Modeling biomolecules: Larger scales, longer durations. John A. Board, Jr., Laxmikant V. Kalé, Klaus Schulten, Robert D. Skeel, and Tamar Schlick. IEEE Computational Science & Engineering, Winter:19-30, 1994.
188. Molecular dynamics on parallel computers: Applications for theoretical biophysics. Thomas C. Bishop, Helmut Heller, and Klaus Schulten. In Rajiv K. Kalia and Priya Vashishta, editors, Toward Teraflop Computing and New Grand Challenge Applications, pp. 129-138. Nova Science Publishers, Inc., New York, 1995.
183. Topology representing network in robotics. Kakali Sarkar and Klaus Schulten. In J. Leo van Hemmen, Eytan Domany, and Klaus Schulten, editors, Models of Neural Networks, volume 3 of Physics of Neural Networks, pp. 281-302. Springer-Verlag, New York, 1996.
176. Multi-mode coupling of protein motion to electron transfer in the photosynthetic reaction center: Spin-boson theory based on a classical molecular dynamics simulation. Dong Xu and Klaus Schulten. In J. Breton and A. Vermeglio, editors, The Photosynthetic Bacterial Reaction Center: II. Structure, Spectroscopy and Dynamics, NATO Science Series A: Life Sciences, pp. 301-312. Plenum Press, New York, 1992.
165. Computational biology on massively parallel machines. Klaus Schulten. In Parallel Computation - Proceedings of the First International ACPC Conference, Salzburg, Austria, pp. 391-400, New York, 1992. Springer.
136. Self-organizing maps and adaptive filters. Helge Ritter, Klaus Obermayer, Klaus Schulten, and Jeanne Rubner. In J. Leo van Hemmen, Eytan Domany, and Klaus Schulten, editors, Models of Neural Networks, Physics of Neural Networks, pp. 281-306. Springer-Verlag, New York, 1991.
112. Mathematica: Mathematik auf Mikrocomputern. Markus van Almsick and Klaus Schulten. MC-Computermagazin, 11:42-59, 1989.
103. Wie neuronale Netwerke Roboter steuern können. Helge Ritter, Thomas Martinetz, and Klaus Schulten. MC-Computermagazin, 2:48-61, 1989.
100. Eine Cray für 100.000 DM. Helmut Grubmüller, Helmut Heller, and Klaus Schulten. MC-Computermagazin, 11:48-64, 1988.
93. Eine Computersimulation künstlicher Wesen - Experimente in einer Welt synthetischer Psychologie. Klaus Boehncke, Christoph Köhler, Georg Meyer-Berg, and Klaus Schulten. MC-Computermagazin, 7:34-48, 1988.
87. "Molecular Design" - Simulation und Graphik von Biomolekülen. Herbert Treutlein, Andreas Windemuth, and Klaus Schulten. MC-Computermagazin, 1:46-57, 1988.
83. Physik und Gehirn - Wie dynamische Modelle von Nervennetzen natürliche Intelligenz erklären. Joachim Buhmann, Robert Divko, Helge Ritter, and Klaus Schulten. MC-Computermagazin, 9:108-120, 1987.
81. Ordnung aus Chaos, Vernunft aus Zufall - Physik biologischer und digitaler Informationsverarbeitung. Klaus Schulten. In B.-O. Küppers, editor, Ordnung aus dem Chaos, pp. 243-268. Piper Verlag, Munich, 1987.
76. Physicists explore human and artificial intelligence. Joachim Buhmann, Robert Divko, Helge Ritter, and Klaus Schulten. In Structure and Dynamics of Nucleic Acids, Proteins and Membranes, pp. 301-328. Plenum Press, 1986.
58. Proton conduction through proteins: An overview of theoretical principles and applications. Zan Schulten and Klaus Schulten. Methods in Enzymology, 127:419-438, 1986.
57. Neuro-kybernetik und künstliche Intelligenz. Joachim Buhmann, Helge Ritter, and Klaus Schulten. Computerwoche, 25, 1985.
45. Magnetfeldeffekte in Chemie und Biologie. Klaus Schulten and Albert Weller. Die Umschau, 25/26:779-783, 1984.
35. Linear polyene electronic structure and potential surfaces. Bruce S. Hudson, Bryan E. Kohler, and Klaus Schulten. In Edward C. Lim, editor, Excited States, volume 6, pp. 1-95. Academic Press, New York, 1982.
34. Magnetic field effects in chemistry and biology. Klaus Schulten. In J. Treusch, editor, Festkörperprobleme, volume 22, pp. 61-83. Vieweg, Braunschweig, 1982.